def __init__(self, fname, genepop_dir=None):
"""Initializes the controller.
genepop_dir is the directory where GenePop is.
The binary should be called Genepop (capital G)
"""
self._fname = fname
self._controller = GenePopController(genepop_dir)
self.__fst_pair_locus = {} #More caches like this needed!
def __init__(self, fname, genepop_dir=None):
"""Initializes the controller.
genepop_dir is the directory where GenePop is.
The binary should be called Genepop (capital G)
"""
self._fname = fname
self._controller = GenePopController(genepop_dir)
def __init__(self, fname, genepop_dir = None):
"""Initializes the controller.
genepop_dir is the directory where GenePop is.
The binary should be called Genepop (capital G)
"""
self._fname = fname
self._controller = GenePopController(genepop_dir)
self.__fst_pair_locus = {} # More caches like this needed!
self.__allele_frequency = {} # More caches like this needed!
class EasyController:
def __init__(self, fname, genepop_dir=None):
"""Initializes the controller.
genepop_dir is the directory where GenePop is.
The binary should be called Genepop (capital G)
"""
self._fname = fname
self._controller = GenePopController(genepop_dir)
self.__fst_pair_locus = {} #More caches like this needed!
def get_basic_info(self):
f = open(self._fname)
rec = GenePop.read(f)
f.close()
return rec.pop_list, rec.loci_list
def test_hw_pop(self, pop_pos, test_type="probability"):
if test_type == "deficiency":
hw_res = self._controller.test_pop_hz_deficiency(self._fname)
elif test_type == "excess":
hw_res = self._controller.test_pop_hz_excess(self._fname)
else:
loci_res, hw_res, fisher_full = self._controller.test_pop_hz_prob(
self._fname, ".P")
for i in range(pop_pos - 1):
hw_res.next()
return hw_res.next()
def test_hw_global(self,
test_type="deficiency",
enum_test=True,
dememorization=10000,
batches=20,
iterations=5000):
if test_type == "deficiency":
pop_res, loc_res, all = self._controller.test_global_hz_deficiency(
self._fname, enum_test, dememorization, batches, iterations)
else:
pop_res, loc_res, all = self._controller.test_global_hz_excess(
self._fname, enum_test, dememorization, batches, iterations)
return list(pop_res), list(loc_res), all
def test_ld_all_pair(self,
locus1,
locus2,
dememorization=10000,
batches=20,
iterations=5000):
all_ld = self._controller.test_ld(self._fname, dememorization, batches,
iterations)[1]
for ld_case in all_ld:
(l1, l2), result = ld_case
if (l1 == locus1 and l2 == locus2) or (l1 == locus2
and l2 == locus1):
return result
def estimate_nm(self):
""" Estimate Nm. Just a simple bridge.
"""
return self._controller.estimate_nm(self._fname)
def get_heterozygosity_info(self, pop_pos, locus_name):
"""Returns the heterozygosity info for a certain locus on a population.
Returns (Expected homozygotes, observed homozygotes,
Expected heterozygotes, observed heterozygotes)
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
pops = list(pop_iter)
return pops[pop_pos][1][locus_name][1]
def get_genotype_count(self, pop_pos, locus_name):
"""Returns the genotype counts for a certain population and locus
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
pop_iter = list(pop_iter)
return pop_iter[pop_pos][1][locus_name][0]
def get_fis(self, pop_pos, locus_name):
"""Returns the Fis for a certain population and locus
Below CW means Cockerham and Weir and RH means Robertson and Hill.
Returns a pair:
dictionary [allele] = (repetition count, frequency, Fis CW )
with information for each allele
a triple with total number of alleles, Fis CW, Fis RH
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
pops = list(pop_iter)
return pops[pop_pos][1][locus_name][2:]
def get_alleles(self, pop_pos, locus_name):
"""Returns the alleles for a certain population and locus.
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
pop_iter = list(pop_iter)
return pop_iter[pop_pos][1][locus_name][2].keys()
def get_alleles_all_pops(self, locus_name):
"""Returns the alleles for a certain population and locus.
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
for locus_info in loc_iter:
if locus_info[0] == locus_name:
return locus_info[1]
def get_allele_frequency(self, pop_pos, locus_name):
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
for locus_info in loc_iter:
if locus_info[0] == locus_name:
alleles = locus_info[1]
pop_name, freqs, total = locus_info[2][pop_pos]
allele_freq = {}
for i in range(len(alleles)):
allele_freq[alleles[i]] = freqs[i]
return total, allele_freq
def get_multilocus_f_stats(self):
""" Returns the multilocus F stats
Explain averaging.
Returns Fis(CW), Fst, Fit
"""
return self._controller.calc_fst_all(self._fname)[0]
def get_f_stats(self, locus_name):
""" Returns F stats for a locus
Returns Fis(CW), Fst, Fit, Qintra, Qinter
"""
loci_iter = self._controller.calc_fst_all(self._fname)[1]
for name, fis, fst, fit, qintra, qinter in loci_iter:
if name == locus_name:
return fis, fst, fit, qintra, qinter
def get_avg_fis(self):
return self._controller.calc_diversities_fis_with_identity(
self._fname)[1]
def get_avg_fst_pair(self):
return self._controller.calc_fst_pair(self._fname)[1]
def get_avg_fst_pair_locus(self, locus):
if len(self.__fst_pair_locus) == 0:
iter = self._controller.calc_fst_pair(self._fname)[0]
for locus_info in iter:
self.__fst_pair_locus[locus_info[0]] = locus_info[1]
return self.__fst_pair_locus[locus]
def calc_ibd(self, is_diplo=True, stat="a", scale="Log", min_dist=0.00001):
if is_diplo:
return self._controller.calc_ibd_diplo(self._fname, stat, scale,
min_dist)
else:
return self._controller.calc_ibd_haplo(self._fname, stat, scale,
min_dist)
class EasyController:
def __init__(self, fname, genepop_dir=None):
"""Initializes the controller.
genepop_dir is the directory where GenePop is.
The binary should be called Genepop (capital G)
"""
self._fname = fname
self._controller = GenePopController(genepop_dir)
def get_basic_info(self):
f = open(self._fname)
rec = GenePop.parse(f)
f.close()
return rec.pop_list, rec.loci_list
def test_hw_pop(self, pop_pos, test_type="probability"):
if test_type == "deficiency":
hw_res = self._controller.test_pop_hz_deficiency(self._fname)
elif test_type == "excess":
hw_res = self._controller.test_pop_hz_excess(self._fname)
else:
loci_res, hw_res, fisher_full = self._controller.test_pop_hz_prob(self._fname)
for i in range(pop_pos - 1):
hw_res.next()
return hw_res.next()
def test_hw_global(self, test_type="deficiency", enum_test=True, dememorization=10000, batches=20, iterations=5000):
if test_type == "deficiency":
pop_res, loc_res, all = self._controller.test_global_hz_deficiency(
self._fname, enum_test, dememorization, batches, iterations
)
else:
pop_res, loc_res, all = self._controller.test_global_hz_excess(
self._fname, enum_test, dememorization, batches, iterations
)
return list(pop_res), list(loc_res), all
def test_ld_all_pair(self, locus1, locus2, dememorization=10000, batches=20, iterations=5000):
all_ld = self._controller.test_ld(self._fname, dememorization, batches, iterations)[1]
for ld_case in all_ld:
(l1, l2), result = ld_case
if (l1 == locus1 and l2 == locus2) or (l1 == locus2 and l2 == locus1):
return result
def estimate_nm(self):
""" Estimate Nm. Just a simple bridge.
"""
return self._controller.estimate_nm(self._fname)
def get_heterozygosity_info(self, pop_pos, locus_name):
"""Returns the heterozygosity info for a certain locus on a population.
Returns (Expected homozygotes, observed homozygotes,
Expected heterozygotes, observed heterozygotes)
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
pops = list(pop_iter)
return pops[pop_pos][1][locus_name][1]
def get_genotype_count(self, pop_pos, locus_name):
"""Returns the genotype counts for a certain population and locus
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
pop_iter = list(pop_iter)
return pop_iter[pop_pos][1][locus_name][0]
def get_fis(self, pop_pos, locus_name):
"""Returns the Fis for a certain population and locus
Below CW means Cockerham and Weir and RH means Robertson and Hill.
Returns a pair:
dictionary [allele] = (repetition count, frequency, Fis CW )
with information for each allele
a triple with total number of alleles, Fis CW, Fis RH
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
pops = list(pop_iter)
return pops[pop_pos][1][locus_name][2:]
def get_alleles(self, pop_pos, locus_name):
"""Returns the alleles for a certain population and locus.
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
pop_iter = list(pop_iter)
return pop_iter[pop_pos][1][locus_name][2].keys()
def get_alleles_all_pops(self, locus_name):
"""Returns the alleles for a certain population and locus.
"""
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
for locus_info in loc_iter:
if locus_info[0] == locus_name:
return locus_info[1]
def get_allele_frequency(self, pop_pos, locus_name):
geno_freqs = self._controller.calc_allele_genotype_freqs(self._fname)
pop_iter, loc_iter = geno_freqs
for locus_info in loc_iter:
if locus_info[0] == locus_name:
alleles = locus_info[1]
pop_name, freqs, total = locus_info[2][pop_pos]
allele_freq = {}
for i in range(len(alleles)):
allele_freq[alleles[i]] = freqs[i]
return total, allele_freq
def get_multilocus_f_stats(self):
""" Returns the multilocus F stats
Explain averaging.
Returns Fis(CW), Fst, Fit
"""
return self._controller.calc_fst_all(self._fname)[0]
def get_f_stats(self, locus_name):
""" Returns F stats for a locus
Returns Fis(CW), Fst, Fit, Qintra, Qinter
"""
loci_iter = self._controller.calc_fst_all(self._fname)[1]
for name, fis, fst, fit, qintra, qinter in loci_iter:
if name == locus_name:
return fis, fst, fit, qintra, qinter
def get_avg_fis(self):
return self._controller.calc_diversities_fis_with_identity(self._fname)[1]
def get_avg_fst_pair(self):
return self._controller.calc_fst_pair(self._fname)[1]
def get_avg_fst_pair_locus(self, locus):
iter = self._controller.calc_fst_pair(self._fname)[0]
for locus_info in iter:
if locus_info[0] == locus:
return locus_info[1]
def calc_ibd(self, is_diplo=True, stat="a", scale="Log", min_dist=0.00001):
if is_diplo:
return self._controller.calc_ibd_diplo(self._fname, stat, scale, min_dist)
else:
return self._controller.calc_ibd_haplo(self._fname, stat, scale, min_dist)
